Tools and information for AMBER and CPPTRAJ examples
Updated: June 12, 2020
Center specified coordinates to box center or onto reference structure. center [<mask>] [origin] [mass] [ reference | ref <name> | refindex <#> [<refmask>]] [<mask>] Center based on atoms in mask; default is all atoms. [origin] Center to origin… Read More
Updated: February 2, 2024
Set or overwrite box information for frames. box {[x <xval>] [y <yval>] [z <zval>] {[alpha <a>][beta <b>][gamma <g>][truncoct]} | nobox | auto [offset <offset> | getbox… Read More
Updated: February 26, 2020
Calculate the min/max coordinates for specified atoms. Can be used to create grid data sets. bounds [<mask>] [out <filename>] [dx <dx> [dy <dy>] [dz <dz>] name <gridname> [offset <bin offset>]] [<mask>] Mask of atoms to determine bounds of…. Read More
Updated: January 12, 2024
Calculate an average structure. Not to be confused with the avg command. average {crdset <set name> | <filename>} [<mask>] [start <start>] [stop <stop>] [offset <offset>] [Trajout Args] <filename> If specified, write averaged coordinates to <filename> (not compatible with… Read More
Updated: April 6, 2023
Automatically re-image coordinates. autoimage [<mask> | anchor <mask> [fixed <mask>][mobile <mask>]] [origin] [firstatom] [familiar | triclinic] [<mask> | anchor <mask>] Atoms to image… Read More
Updated: January 26, 2024
Attempt to create a map between atoms in molecules with different atom ordering. atommap <target> <reference> [mapout <filename>] [maponly] … Read More
Updated: January 26, 2024
Compute the atomic positional fluctuations. atomicfluct [<name>] [out <filename>] [<mask>] [byres [pdbres] | byatom | bymask] … Read More
Updated: March 27, 2019
Calculate average correlation between motions of specified atoms. atomiccorr [<mask>] out <filename> [cut <cutoff>] [min <min spacing>] [byatom | byres] <mask> Atoms to calculate motion vectors for. out <filename> File to write results to. cut <cutoff> Only print… Read More
Updated: March 27, 2019
Calculate area per molecule for molecules in a specified plane. areapermol [<name>] {[<mask1>] [nlayers <#>] | nmols <#>} [out <filename>] [{xy | xz | yz}] [<name>] Data set name. [<mask1>] Atom mask for selecting molecules. If any atom… Read More
Updated: July 23, 2020
Calculate the angle between three points angle [<dataset name>] <mask1> <mask2> <mask3> [out <filename>] [mass] [<dataset name>] Output data set name. <maskX> Three atom masks selecting atom(s) to calculate angle for. [out <filename>] Output file name. [mass] Use… Read More
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